Author: christophgil-guest Date: 2012-12-18 22:25:36 +0000 (Tue, 18 Dec 2012) New Revision: 12694
Removed: trunk/packages/strap-base/trunk/debian/templates/ Modified: trunk/packages/strap-base/trunk/debian/copyright trunk/packages/strap-base/trunk/debian/strap_base.1 trunk/packages/strap-base/trunk/debian/strap_to_clustal.1 trunk/packages/strap-base/trunk/debian/strap_to_fasta.1 trunk/packages/strap-base/trunk/debian/strap_to_html.1 trunk/packages/strap-base/trunk/debian/strap_to_msf.1 trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1 trunk/packages/strap-base/trunk/debian/strap_to_word.1 Log: Simplified copyright. Updated man pages Modified: trunk/packages/strap-base/trunk/debian/copyright =================================================================== --- trunk/packages/strap-base/trunk/debian/copyright 2012-12-18 22:18:34 UTC (rev 12693) +++ trunk/packages/strap-base/trunk/debian/copyright 2012-12-18 22:25:36 UTC (rev 12694) @@ -21,21 +21,12 @@ ******************************************************************************** Files: debian/* Copyright: © 2012 Christoph Gille License: GPL-3 # ******************************************************************************** -Files: 3d.png browser16.png ledgreen16.png +Files: 3d.gif browser16.gif ledgreen16.gif Source: http://www.phoca.cz/demo/gallery-categories/category/22-nuvola-icons License: LGPL-2.1 Comment: On Debian systems, the complete text of the Apache license can be found in '/usr/share/common-licenses/LGPL-2.1' # ******************************************************************************** - -File: visible.png 1.png border_color.png compact_camera.png edit.png - home.png scales.png stack_of_photos.png zip.png console.png end.png - import.png mac_os.png scissors.png bug.png search.png umbrella.png - apply16.png clipboard.png cursor_hand.png folder.png keyboard.png - pdf.png services.png wifi.png close.png delete.png - ruler.png settings2.png dna_helix.png globe.png - lifebuoy.png sandglass.png settings2_26.png windows.png attach.png - download.png line_chart.png save_as.png skip_to_start.png word.png - add.png +Files: *.png Source: http://icons8.com/ http://www.visualpharm.com/ Citation from Web-site: Use Policy You can use it for your websites and applications for free. Just link to either You can’t modify the @@ -44,15 +35,15 @@ # ******************************************************************************** -File: astex.png +File: astex.gif Source: http://openastexviewer.net/ License: LPGL # ******************************************************************************** -File: jmol.jpg +File: jmol.gif Source: http://sourceforge.net/projects/jmol/ License: LGPLv2 # ******************************************************************************** -File: pfam.png +File: pfam.gif Source: pfam.sanger.ac.uk/ License: Creative Commons Zero ("CC0") licence. # ******************************************************************************** Modified: trunk/packages/strap-base/trunk/debian/strap_base.1 =================================================================== --- trunk/packages/strap-base/trunk/debian/strap_base.1 2012-12-18 22:18:34 UTC (rev 12693) +++ trunk/packages/strap-base/trunk/debian/strap_base.1 2012-12-18 22:25:36 UTC (rev 12694) @@ -1,4 +1,4 @@ -.\"" Do not edit this file. It has been generated from templateGui.1 with /usr/bin/gpp +.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes. .TH Strap 1 "October 2011" .SH NAME @@ -135,8 +135,13 @@ -script="open_3D viewName, *" would display all proteins with 3D-coordinates three-dimensionally (See -v3d=). Scripts consisting of more than one line should be -stored in a file and the file path or URL should be given. +stored in a file and the file path or URL should be given. +If scripts are run on a server which allows many instances simultaneously, +consider to use a database backend instead of the file based cache for computed results +(See http://www.bioinformatics.org/strap/cache.html) + + Example: -script2="open_3D viewName, *" -script3="3D_select $ALL" -script7="3D_ribbons on" -script8="superimpose *" @@ -198,16 +203,11 @@ \fB\-noCache\fR - Do not use cached results of previous +Do not use cached results of previous computations. This setting can be changed in the graphical user interface with a check-box. +Also see http://www.bioinformatics.org/strap/cache.html. -This setting influences the result of searches in growing -databases. For example consider the similarity search method -Blast. With the cache turned on, Strap would present a previously -computed Blast result even though new sequences might have been -published since last run. - \fB\-keepFiles\fR Do not delete temp-files after the session. This is only important for @@ -268,6 +268,23 @@ is deactivated. +.SH Parameters for the Java virtual machine + +Even if Strap is started indirectly with a UNIX script file, +parameters can still be passed directly to the Java command. +Those parameters need to be prefixed with "JVM_". +This does not (yet) work for MS-Windows. + + +Examples: + +\fB JVM_-Xmx200M\fR +\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR +\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR +\fB JVM_-ea\fR + + + .SH ALIGNMENT FILE GENERATION With the options \fB\-toMultipleFasta\fR or \fB\-toClustal\fR or Modified: trunk/packages/strap-base/trunk/debian/strap_to_clustal.1 =================================================================== --- trunk/packages/strap-base/trunk/debian/strap_to_clustal.1 2012-12-18 22:18:34 UTC (rev 12693) +++ trunk/packages/strap-base/trunk/debian/strap_to_clustal.1 2012-12-18 22:25:36 UTC (rev 12694) @@ -1,4 +1,4 @@ -.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp +.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes. .TH strap_to_clustal 1 "Mai 2012" .SH NAME strap_to_clustal \- Reads amino acid sequences and creates a multiple sequence alignment file in clustal format. @@ -66,14 +66,34 @@ the secondary structure to be displayed. This information is provided with script commands. See http://www.bioinformatics.org/strap/strap4services.html for details. -.SH LIMITATIONS +If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default +file based cache. This is described in http://www.bioinformatics.org/strap/cache.html. -Currently, the cache for alignment results should be accessed only by one instance at a time. -If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted. -Workaround: Deactivate the cache with the option -noCache. -If you do need a cache in a web server environment, please send a request for feature to the author. + + + +.SH Parameters for the Java virtual machine + +Even if Strap is started indirectly with a UNIX script file, +parameters can still be passed directly to the Java command. +Those parameters need to be prefixed with "JVM_". +This does not (yet) work for MS-Windows. + + +Examples: + +\fB JVM_-Xmx200M\fR +\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR +\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR +\fB JVM_-ea\fR + + + + + + .SH HOME-PAGE http://3d-alignment.eu/ Modified: trunk/packages/strap-base/trunk/debian/strap_to_fasta.1 =================================================================== --- trunk/packages/strap-base/trunk/debian/strap_to_fasta.1 2012-12-18 22:18:34 UTC (rev 12693) +++ trunk/packages/strap-base/trunk/debian/strap_to_fasta.1 2012-12-18 22:25:36 UTC (rev 12694) @@ -1,4 +1,4 @@ -.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp +.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes. .TH strap_to_fasta 1 "Mai 2012" .SH NAME strap_to_fasta \- Reads amino acid sequences and creates a fasta formated sequence file for each sequence. Modified: trunk/packages/strap-base/trunk/debian/strap_to_html.1 =================================================================== --- trunk/packages/strap-base/trunk/debian/strap_to_html.1 2012-12-18 22:18:34 UTC (rev 12693) +++ trunk/packages/strap-base/trunk/debian/strap_to_html.1 2012-12-18 22:25:36 UTC (rev 12694) @@ -1,4 +1,4 @@ -.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp +.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes. .TH strap_to_html 1 "Mai 2012" .SH NAME strap_to_html \- Reads amino acid sequences and creates an alignment view for web browsers. @@ -74,6 +74,12 @@ In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and the secondary structure to be displayed. This information is provided with script commands. See http://www.bioinformatics.org/strap/strap4services.html for details. + +If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default +file based cache. This is described in http://www.bioinformatics.org/strap/cache.html. + + + .SS Residue annotations in HTML alignment output. Residue positions to be highlighted in the html output need to @@ -83,14 +89,28 @@ used to attach information. The script may also be used to define the [gapped] amino acid sequences. -.SH LIMITATIONS -Currently, the cache for alignment results should be accessed only by one instance at a time. -If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted. -Workaround: Deactivate the cache with the option -noCache. -If you do need a cache in a web server environment, please send a request for feature to the author. +.SH Parameters for the Java virtual machine +Even if Strap is started indirectly with a UNIX script file, +parameters can still be passed directly to the Java command. +Those parameters need to be prefixed with "JVM_". +This does not (yet) work for MS-Windows. + + +Examples: + +\fB JVM_-Xmx200M\fR +\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR +\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR +\fB JVM_-ea\fR + + + + + + .SH HOME-PAGE http://3d-alignment.eu/ Modified: trunk/packages/strap-base/trunk/debian/strap_to_msf.1 =================================================================== --- trunk/packages/strap-base/trunk/debian/strap_to_msf.1 2012-12-18 22:18:34 UTC (rev 12693) +++ trunk/packages/strap-base/trunk/debian/strap_to_msf.1 2012-12-18 22:25:36 UTC (rev 12694) @@ -1,4 +1,4 @@ -.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp +.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes. .TH strap_to_msf 1 "Mai 2012" .SH NAME strap_to_msf \- Reads amino acid sequences and creates a multiple sequence alignment file in msf format. @@ -66,14 +66,34 @@ the secondary structure to be displayed. This information is provided with script commands. See http://www.bioinformatics.org/strap/strap4services.html for details. -.SH LIMITATIONS +If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default +file based cache. This is described in http://www.bioinformatics.org/strap/cache.html. -Currently, the cache for alignment results should be accessed only by one instance at a time. -If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted. -Workaround: Deactivate the cache with the option -noCache. -If you do need a cache in a web server environment, please send a request for feature to the author. + + + +.SH Parameters for the Java virtual machine + +Even if Strap is started indirectly with a UNIX script file, +parameters can still be passed directly to the Java command. +Those parameters need to be prefixed with "JVM_". +This does not (yet) work for MS-Windows. + + +Examples: + +\fB JVM_-Xmx200M\fR +\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR +\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR +\fB JVM_-ea\fR + + + + + + .SH HOME-PAGE http://3d-alignment.eu/ Modified: trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1 =================================================================== --- trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1 2012-12-18 22:18:34 UTC (rev 12693) +++ trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1 2012-12-18 22:25:36 UTC (rev 12694) @@ -1,4 +1,4 @@ -.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp +.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes. .TH strap_to_multiple_fasta 1 "Mai 2012" .SH NAME strap_to_multiple_fasta \- Reads amino acid sequences and creates a multiple fast file. @@ -66,14 +66,34 @@ the secondary structure to be displayed. This information is provided with script commands. See http://www.bioinformatics.org/strap/strap4services.html for details. -.SH LIMITATIONS +If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default +file based cache. This is described in http://www.bioinformatics.org/strap/cache.html. -Currently, the cache for alignment results should be accessed only by one instance at a time. -If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted. -Workaround: Deactivate the cache with the option -noCache. -If you do need a cache in a web server environment, please send a request for feature to the author. + + + +.SH Parameters for the Java virtual machine + +Even if Strap is started indirectly with a UNIX script file, +parameters can still be passed directly to the Java command. +Those parameters need to be prefixed with "JVM_". +This does not (yet) work for MS-Windows. + + +Examples: + +\fB JVM_-Xmx200M\fR +\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR +\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR +\fB JVM_-ea\fR + + + + + + .SH HOME-PAGE http://3d-alignment.eu/ Modified: trunk/packages/strap-base/trunk/debian/strap_to_word.1 =================================================================== --- trunk/packages/strap-base/trunk/debian/strap_to_word.1 2012-12-18 22:18:34 UTC (rev 12693) +++ trunk/packages/strap-base/trunk/debian/strap_to_word.1 2012-12-18 22:25:36 UTC (rev 12694) @@ -1,4 +1,4 @@ -.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp +.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes. .TH strap_to_word 1 "Mai 2012" .SH NAME strap_to_word \- Reads amino acid sequences and creates an alignment view which can be edited in a word processor. @@ -65,6 +65,12 @@ In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and the secondary structure to be displayed. This information is provided with script commands. See http://www.bioinformatics.org/strap/strap4services.html for details. + +If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default +file based cache. This is described in http://www.bioinformatics.org/strap/cache.html. + + + .SS Residue annotations in HTML alignment output. Residue positions to be highlighted in the html output need to @@ -74,14 +80,28 @@ used to attach information. The script may also be used to define the [gapped] amino acid sequences. -.SH LIMITATIONS -Currently, the cache for alignment results should be accessed only by one instance at a time. -If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted. -Workaround: Deactivate the cache with the option -noCache. -If you do need a cache in a web server environment, please send a request for feature to the author. +.SH Parameters for the Java virtual machine +Even if Strap is started indirectly with a UNIX script file, +parameters can still be passed directly to the Java command. +Those parameters need to be prefixed with "JVM_". +This does not (yet) work for MS-Windows. + + +Examples: + +\fB JVM_-Xmx200M\fR +\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR +\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR +\fB JVM_-ea\fR + + + + + + .SH HOME-PAGE http://3d-alignment.eu/ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
